Blastn plus jupyter on Docker
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Examples from bioinformatics - using containers for bioinformatics tools (such as blastn), plus example Jupyter notebooks
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Blastn plus jupyter on Docker
- 1. Blastn + Jupyter on Docker Examples from Bioinformatics Samantha & Lynn Langit
- 2. “ ” Jupyter - Inspired by Mathematica Thanks Steven Wolfram If you can SEE it (your data and code), you can work with it better @lynnlangit
- 3. Next terminal <- a better Python REPL • Fernando Perez in 2001 • IPython (interactive) • Modeled - Mathematica Notebooks • IP(y): Notebook -> in a browser • 2012 IPython -> Jupyter Notebook @lynnlangit
- 5. Jupyter Notebooks supports ML Lifecycle 1. Collect Data Retrieve Files Query SQL Databases Call Web Services “Scrape” Web Pages 2. Prepare Data Explore Data Validate Data Clean Data Features / Data 4. Evaluate Model Test Performance Compare Models Validate Model Visualize 5. Deploy Model Export Model File Prepare Job Deploy Container Re-package Model Execute code blocks: - Python, R… code - SQL queries - Shell commands 3. Train Model Prepare Training Set Experiment Test Model Visualize Write Documentation: - Markdown language Visualize Data - Viz tools…
- 6. Jupyter Visualizations – so many possibilities
- 7. Notebook Customizations Multiple Runtimes Languages Share output Code or Equations LaTex Math Comments Markdown Wiki-like Graphics Visualizations Charting Results LIVE DOCUMENTATION Reproducible Research @lynnlangit
- 9. Mathematica evolved… Jupyter Notebook Market leader Started for single use Academic community GitHub integration Added Jupyter Hub for collaboration Zeppelin Notebook Start for collaboration Enterprise Security Vendor Notebook Databricks for Apache Spark Jupyter-like, but proprietary format @lynnlangit
- 10. Running Notebooks Desktop Install and run Local Server Can use Jupyter Hub for groups Cloud Large number of options @lynnlangit Docker Start a container
- 11. Extending, Refactoring Open Notebooks • Write functions in one notebook • Link to another notebook • Write extensions (nbextensions.com)
- 12. Up the bar Personalized medicine via genomic analysis @lynnlangit
- 13. Reproducible Research – Experiments as Code @lynnlangit
- 14. What is Blastn? Basic Local Alignment Search Tool - BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
- 16. Cloud-based Jupyter PaaS • AWS SageMaker • Azure Notebooks • Google Colabs Wireframe that first the role of UX in agencies @lynnlangit
- 18. Tools for Jupyter • Binder for GitHub • Point to your GitHub Repo • Jupyter Notebooks • Requirements.txt • It builds a Docker image • You can run your Notebooks @lynnlangit
- 20. Example - GT-Scan2 Jupyter for Genomics Research @lynnlangit
- 21. Future of Jupyter for Research Academic Institutions and Research Labs UC Berkeley, Davis, San Diego Cal Poly San Luis Obispo Clemson University UC Boulder U of Illinois, Minnesota, Missouri, Rochester, Texas MIT Michigan State U Texas A & M @lynnlangit
Editor's Notes
- History talk from Cristian Prieto (NDC Oslo 2016) -- https://vimeo.com/223984769 http://blog.fperez.org/2012/01/ipython-notebook-historical.html
- Local install pip install –iPython all -OR- can use anaconda, which installs Jupyter notebooks by default pip install jupyter[all] and you can pip install R You can use Docker – 2.1 GB image contains all libraries or you can use Azure Notebooks or AWS SageMaker Notebooks Only Python2 is installed by default, you can install other runtimes Start and run in local browser (no database, uses local .json files) IPython notebook -> localhost:8888/tree Use GitHub-flavor Markdown (by default) https://dwhsys.com/2017/03/25/apache-zeppelin-vs-jupyter-notebook/
- https://github.com/ipython-contrib/jupyter_contrib_nbextensions pip install jupyter_contrib_nbextensions –OR- conda install -c conda-forge jupyter_contrib_nbextensions
- https://github.com/Microsoft/Elevation/blob/master/notebooks/aggregation.ipynb https://www.microsoft.com/en-us/research/project/crispr/
- https://blast.ncbi.nlm.nih.gov/Blast.cgi
- https://hub.docker.com/r/lynnlangit/blastn-jupyter-docker/
- https://medium.com/@lynnlangit/aws-sagemaker-for-bioinformatics-b8e8a96479d8 Jupyter on GCE VM -- https://towardsdatascience.com/running-jupyter-notebook-in-google-cloud-platform-in-15-min-61e16da34d52
- https://mybinder.org/ -ALSO- https://nbviewer.jupyter.org/ - allows you to run notebooks stored in GitHub
- http://jupyterhub-tutorial.readthedocs.io/en/latest/ https://github.com/jupyterhub/jupyterhub-tutorial/blob/master/JupyterHub.pdf http://jupyterhub.readthedocs.io/en/latest/gallery-jhub-deployments.html